Shadow of a Doubt
by Fluxolotl
Summary: It's been fifty years since Shadow was put into stasis, and Black Doom has decided it's time to retrieve him and refine him as the ultimate weapon. Will Shadow give in to his blood relatives? Or will he forge his own path, attracting the eyes of G.U.N.? (Set in an alternate universe.)
1. Chapter 1: Awakening

Silence reigned in the cold, dark room. Situated underground beneath a secret government building just outside Westopolis, various experiments were kept confined in the concrete walls, far away from the public eye. The majority of these experiments were created as potential weapons of mass destruction should wars ever arise. All of them had been kept in glass cryogenic stasis tubes down here for years, some even decades.

Three tubes in particular contained the beings most important to the now deceased brilliant scientist, Gerald Robotnik--his prototype of the "Ultumate Lifeform Project" (or U.L.P.) the Biolizard; his granddaughter, Maria; and the final product of the U.L.P., "Shadow."

Looking at the alpha and the omega of the U.L.P., it would be understandable for one to not believe that the Biolizard and Shadow were related other than in size. The Biolizard was made as a female reptilian creature clad with orange and navy blue scales and armed with a large life support machine strapped to her back, tubes snaking from the center and digging into her temples and ribs, delivering some unidentifiable fluid throughout her artificial veins. Shadow, on the other hand, was modeled after a male anthropomorphic hedgehog. With black fur with large patches of red scales, his organs run on blood from the alien race known as the Black Arms. He has no need for a life support system and can manage well on his own, though he's always appreciated the company of Maria, who he sees as an older sister.

Today, a certain someone would reveal themselves as his biological sibling...

A black and red creature not unlike Shadow skittered its way over the cool tile flooring out from a dark corner of the room, a whiplike tail trailing behind. It was on a mission to retrieve its "brother" from stasis on Earth after nearly half a century.

The creature punched in the numbers it was told to earlier that day into the base of the tall cryogenic machine, and a smirk appeared on its muzzle as the glass casing clicked and began to recede upwards. This was the moment its father--Shadow's biological father--Black Doom had been waiting for after a long, long time.

A visible freezing air poured out the base of the machine and the small black and red hedgehog was left out to thaw. A thin veil of ice covered his body, and the creature standing by became disappointed at the realization it would take a while before the two could finally speak. So, it waited.

And waited.

...And waited.

After several hours, the alien entity was growing frustrated with the situation. Shadow's breath and heartbeat had grown slightly more rapid, but no sign of regained consciousness had arrived yet. He remained on the floor, eyes shut tight. No amount of nudging or whispering was of use, and the figure wasn't about to make itself known by yelling. So, it waited some more.

It was finally dusk as evidenced from the narrow windows way up near the ceiling...and Shadow finally stirred.

The alien-hedgehog wearily pulled his eyelids up and looked around the dull, unfamiliar room. He glanced to his left to see his only two friends still frozen, and he let out a sigh of relief that they were essentially in the same situation he was. Shadow then glanced to the right to see a dark figure approaching him, and jumped back in fear.

"Hey, no need to be scared of me, brother," it finally spoke. "I'm here to take you home!"

Shadow stared at this stranger with suspicion. "What do you mean, 'brother?' Where am I? Who are you? Are Maria and Bio alright?"

The stranger laughed. "Dad said it had been fifty years, so no wonder you're full of questions! But I suppose it is impolite of me to not even introduce myself. I'm Eclipse, the Darkling formed from the blood of the very alien leader you were--the mighty Black Doom!"

Raising a confused eyebrow, Shadow looked at Eclipse, and then himself. They did have similar colors at least, but he wasn't quite convinced they were related, much less knew who this "mighty Black Doom" was. He raised the question, resulting in a very offended-looking Eclipse.

"You're not even the slightest bit familiar with dad?! Wow, you're a lot more blissfully ignorant than I thought. He's only, y'know, one of the most powerful alien leaders EVER. You should feel proud he was willing to give some Black Arms blood to your creator. He doesn't exactly go around giving samples to people willy-nilly, ya know. What he does is destroy worlds and conquer armies! Enslave the powerless and roll in wealth!" Eclipse accompanied his monologue with exaggerated hand gestures, trying to implicate just how important Doom should be to Shadow. Shadow, however, was still utterly lost.

While the Darkling rambled on to his own accord, Shadow slid over and hesitantly removed a single Inhibitor Ring from his left wrist, then proceeded to punch the glass of the two tubes containing his lifelong friends until they shattered.

Eclipse stared in awe as Shadow clamped the Inhibitor Ring back around his wrist, breathing heavily as he watched the young girl and android lizard collapsed to the bases of their tubes, frosted over. "Wh...what was that?!"

"Inhibitor Rings...they greatly limit my power so I won't...go berserk..." Shadow muttered. "If I remove even one, my strength increases tenfold..."

"Whaaaaaaaat! Get outta town, that's awesome!" Eclipse's eyes sparkled with a childlike wonder as he jumped up and down around the hedgehog. "I wanna see you remove all four! You'd be amazing if you were back with the Arms!"

"Don't...get so cocky. After what happened only once, I...never wanna let myself get like that again." Shadow sat on the stone floor, a curious Eclipse sitting down next to him. "Like what?" the latter inquired.

Shadow sighed, knowing this creature wouldn't shut up unless he told him the story, and thus began to reflect on his final memory before having been shoved into stasis. He had a hard time believing it had already been fifty years since the incident.

"Well...I want to start by saying Maria is the most important person in my life. To me, at least. She taught me everything I know and gave me the name that even you know me by. I have never known life without her. Or Professor Gerald, for that matter, but after what happened, I'm glad to be away from him. I doubt he's still alive, anyway."

"He was executed, I heard," Eclipse remarked. "He's been dead since a few months after you were put in stasis, I think."

"...Good. Thanks for telling me." Shadow continued. "Anyway, shortly before this happened, Maria was sent down the hall to her room. Immediately I knew something was off, as the professor never made her leave for any experiments he did on me. Maria was always kept around to walk me through the steps of whatever task I had to perform. But this time...no. This was so, so radically different from anything the Prof ever did to me before. He had me sit down and he commented how he was disappointed in the "goody-two-shoes" I had become from being around Maria all the time, and that I was supposed to be a military-grade weapon with no sympathy for the enemy. He then injected me with...something, I'm not sure what...and immediately I felt nothing but pain all over. I felt myself grow larger and develop claws and fangs and a long tail...I felt like I had a huge amount of stored power I needed to unleash as soon as possible. Apparently I had cried out, as Maria came rushing in with these Inhibitor Rings in her hands, and closed them around my wrists and ankles before I could figure out what to do with myself. These things were originally made for Bio in case her power grew unstable, really, but I think Maria did the right thing in giving them to me. After a few seconds I started shrinking back to my normal size, and I just felt super exhausted. Everything was hurting, and here Gerald was screaming at Maria telling her what she did was wrong, that she wasn't supposed to know...next thing either of us were aware of, he was pushing us into cold glass cases saying it would be better if he worked by himself. And then, I woke up here."

Eclipse blinked, processing everything. "Wow. That's...intense, really. Even one as ruthless as Black Doom ensures his underlings are comfortable. I'm...sorry to hear that."

"Honestly, it's none of your concern. This was half a century ago." Shadow gazed down at the stone tile floor. "What was done was done. And if it hadn't been done, I probably would have destroyed everything on the ARK myself...including Maria. That's not a possibility I want to think about."

"The ARK?" Eclipse gave Shadow a puzzled look.

"Yes. The Space Colony ARK. That's where Bio's life and my own life were spent. It was essentially Gerald's secret laboratory. This room is the first time I've experienced someplace else, actually...are we on Earth?"

"Neat, and indeed we are! It's nice here, buuut...I was kinda sent to bring you back into space with dad," replied Eclipse, laughing nervously.

Shadow jumped a little at that last statement. He just woke up on Earth a few minutes ago, and now he's going to be dragged back into space? He wasn't having any of that. Not after all the wonderful stories Maria told him about Earth. "Uh, no. I don't think so. I'd rather stay down here with Maria. Besides, why should I trust you when we've only known each other for less than ten minutes?"

The hedgehog had a point. This was going to be tougher than expected. "Tell ya what," Eclipse sighed, "I'll let you stay here for...one week. I can join you, but first I'll have to go back and tell dad. I know he's gonna be angry with the delay as is, but if I don't tell him about staying here a while beforehand, I'll be toast."

Crossing his arms, Shadow grimaced at his alien relative. "Fine. No funny business, though."

The room returned to silence as the two assessed their situation, waiting for Maria and Biolizard to thaw.


	2. Chapter 2: Enter Rouge

I apologize greatly for the delay in getting this out! I had hit a bit of a block on where exactly to take the story, and I also ended up busy with other things. But I think I've finally figured out a direction to take this. :D

Without further ado, enjoy!~*

Sunlight began to filter in through the high windows, rays landing on the two black and red individuals laying down in the center of the room. Shadow and Eclipse had fallen asleep waiting for the remaining two that were in stasis to regain consciousness. And at last, Shadow was given a rude awakening--not by Eclipse, either.

"Shadow! Wake up! Where are we?"

The hedgehog grunted, preferring to sleep a while longer. He was about to shift to a more comfortable position, but then it hit him. "Maria!" He sat up, reluctantly prying his eyes open. The two stared at each other for a moment, smiling, glad to know the other was safe. Shadow then remembered just where he was. "Oh, um, we're on Earth. I think. This guy says his name is Eclipse and that he's my 'brother,' though I'm not sure whether to believe him. He told me we've been in stasis for...quite a while."

"He sure is odd-looking," Maria commented. "But it is funny, he has the same colors as you. Maybe he's telling the truth?"

The voices caused Eclipse to wake up as well, and he tiredly responded. "Heh, so you guys are no longer icicles." He yawned and rubbed his eyes. "Yeah, this is Earth, and you lot have been frozen for about fifty years now. Welcome to the twenty-first century!"

Maria looked at Eclipse in disbelief. "Fifty years?!" she exclaimed. "But...that means..."

Eclipse knew where she was going with this. "Your grandfather was discovered and executed by the government, and your brother grew up to be an evil scientist who wants to take over the world. Yeah. Also, I'm here to take Shadow back to Black Doom. He's being kinda stubborn about it though, so I guess I'll stay with you all for about a week so we can get to know each other." He stood up and stretched, oblivious to how the sudden news was causing tears to well up in the blonde-haired girl's eyes. Shadow hugged her for comfort and glared at Eclipse, who simply shrugged with a blank expression.

"Everything will be alright, Maria," Shadow said softly. "The professor wasn't as good of a person as he led you to believe, anyway."

Standing a few feet away, the Biolizard (or "Bio," as she preferred to be called) quietly analyzed her surroundings. She wasn't quite sure what to make of the new guy, and wondered what it was he and this "Black Doom" wanted with Shadow, along with just how he knew about the fates of Gerald and his grandson Ivo. She had a hard time believing anyone in the Robotnik family could actually be evil. Rather than asking, however, Bio decided to wander around as the other cryogenic tubes caught her eye. If Ivo were truly up to no good, then surely something around here would prove it.

Shadow caught her long orange tail disappearing around the corner and let go of Maria. "Hey, Bio! Where do you think you're going?!" He quickly stood up and chased after the lizard. Maria wiped her eyes on her sleeve and followed out of curiosity.

Eclipse was left on his own. After making Shadow's friend upset, he settled that this would probably be a good time to leave the building and head off to alert Doom. He skittered his way up the stairs and went through the thick metal door as silently as possible. He gently closed the door behind him, yet a click still sounded, stopping Shadow in his tracks. He rolled his eyes. "Great. He left us."

Bio didn't notice as she was distracted by a particular tube, containing what appeared to be a small robot. She looked at the neatly-written label on the base of the glass. "Gizoid," she read aloud. That name sounded familiar. The date written was only about a year ago, so Gerald couldn't have had anything to do with it.

Maria and Shadow caught up with her and looked at the metallic orange humanoid she had been investigating. "...Gizoid?" Maria asked. "Didn't grandpa say something about finding one of those once?"

Shadow nodded in agreement. "From what I remember, it's an artificial life form made by an ancient civilization. Supposedly some sort of high-tech weapon. It was rumored to 'awaken' once in possession of all seven Chaos Emeralds."

Bio shuddered. Artificial life form? High-tech weapon? That sounded eerily similar to the purpose Gerald intended for herself and Shadow. Maybe this thing was the professor's inspiration, and now, his grandson's...she shook her head. "It's kinda giving me the creeps. Let's go look at the other experiments."

Eclipse had made his way through the monotone tiles of the building, pleased with himself as he had destroyed the place's security system. He took a proud stance when he stood outside in the grass to greet the six small creatures waiting for him.

"Hey guys! Don't worry, I'm back safe and sound. I know I don't have Shadow with me, but we've gotta get back to dad. I managed to get some... interesting details."

The critters murmured. They couldn't speak, as they were genetically modified Wisps--tiny, mute alien beings containing unbelievable power. Of course, these six had been enhanced with Black Arm genes, making their abilities compatible with what would normally be their natural enemies. (Black Doom and the Mother Wisp kind of have a bitter rivalry with each other. You wouldn't expect a giant pink, flowery jellyfish to be so powerful, but she had obliterated many troops effortlessly when the Black Arms first attempted to invade Planet Wisp.) Hovering in front of Eclipse, in order, were: Cregal, a Crimson Wisp; Blurk, a Blue Wisp; Livo, an Ivory Wisp; Purzy, a Purple Wisp; Cyzer, a Cyan Wisp; and Rhygen, a Magenta Wisp.

They at least understood the Darkling's words, however, and Cyzer prepared itself to fuse with him, as the Cyan Laser ability can send an individual from one location to another in mere seconds.

"Laser!" Eclipse commanded, and the snakelike mutant Wisp dissolved itself into Hyper-Go-On particles, surrounding and finally combining with Eclipse, shooting themselves upwards in the direction of the Black Colony. The other five Wisps rapidly followed the bright blueish-green trail.

It was a busy day as usual for government spy Rouge the Bat. Today she had been tasked with locating the current whereabouts of Doctor Eggman by the President, and she wasn't about to disappoint. Rumor had it that the Doctor had uncovered old blueprints from his grandfather, detailing something known simply as "Project Shadow." Whatever it was, it sounded mysterious, and Rouge was certainly all for mystique.

Despite her assignment being to look for the mad scientist, she had decided to do some research on the experiment beforehand. The only file that came up after a solid hour of web searches was a flyer detailing plans for some sort of hybrid creature that was to be given life with alien blood, along with a black-and-white image of a reptilian face. Some notes were left attached to the digital file stating that Project Shadow had been safely contained in a high security building just outside of downtown Westopolis. Rouge knew it was now her top priority to retrieve the experiment before Eggman could get his grubby oil-stained hands on it.

Westopolis wasn't very far from Central City, so combined with her powerful wings, it didn't take long for the bat to locate an inconspicuous concrete building sitting in the grass about half a mile outside the cluster of skyscrapers. That had to be the place. She swooped down to the grey structure and contemplated the metal door now standing in front of her. Surely this place would be on high alert if she attempted to enter.

Nonetheless, it was worth a shot. She cautiously turned the knob. The door was heavier than expected, but it opened with no other issue. Rouge glanced around in front of her, waiting for alarms, bells, lasers, something. But it remained quiet. All that was laid out in front of her was a dark hallway lined with fake plants and inoperable sconces, ending with a bend to the left. She sighed and tip-toed down the winding corridor, ears swiveling to catch any sign of security catching her.

At last she reached another thick, metal door, and still everything was silent. The bat held her breath and reached for the steel handle.

The door creakily opened up to reveal an almost impossibly large room, filled wall to wall with lines of towering tubes containing an array of otherworldly objects--and even beings. Jackpot, Rouge thought to herself, a smirk appearing on her face. She skipped the staircase leading to the floor completely and instead hovered to the other end of the room. Upon reaching the ground, however, she took immediate notice that all three of the glass tubes in front of her were open: one having been unsealed normally, while the other two were shattered.

A lump formed in her throat. She may not have been detected by security, but she feared her fate here might be worse than any authority capturing her. Who knows what beasts lurked down here that could break through two whole inches of glass? She had to leave immediately. She had to tell the Pres--

"Are you looking for something, miss?" a young girl's voice called out from behind. Rouge flinched and turned around to see a tired-looking blonde girl dressed in a simple blue outfit. At least it wasn't the monster she'd anticipated.

"Oh! Yes, indeed. I'm looking for the...'Project Shadow,' whatever that is." Rouge was concerned the little girl had no clue what she was talking about.

"You're looking for Shadow? He's right here! Shadow, we have a visitor!" the girl shouted. Within seconds, around the corner came the most interesting sight Rouge had seen in a while: a dark, messy-furred creature resembling a hedgehog covered in patches of red scales and bearing claws. The two stared at each other for a moment, and then Shadow finally crossed his arms and spoke up.

"Let me guess. You're someone ELSE who wants to take me away for Gaia-knows-what reason? Get in line; I apparently have an audience with an alien warlord--who happens to be my father--in about a week."

The bat was less than prepared for that response, but she made an attempt to reply anyway. She decided to ignore the alien part. "Well, yes, in a way. But if I don't get you out of here myself, then you'll be found out by a mad scientist who wants to use you as a weapon of mass destruction."

Shadow closed his eyes and let out a small chuckle. "That's exactly what the aliens are wanting to do with me. Nothing new there. Seems everyone's after me like hot cakes." He sighed and opened his eyes again, looking at Rouge once more. "Though, I do suppose you'd be the better choice to get out of here with. As long as you're not planning anything funny."

This was easier than Rouge thought. She nodded. "I promise. Now how about we get the heck outta dodge?"

The trio headed back towards the staircase, though Shadow decided to first call out to his remaining friend. "Hey, Bio! Someone's here to let us out. You coming?"

The lizard looked in his direction, hesitating before finally responding. "I...think I'll just stay here, actually. I'm not sure how well the general public would receive a man-made reptile with a giant life support machine on its back and tubes in its head. I'm better off with these other experiments. I'm just a prototype, anyway. You're a better version of me. You should go on ahead."

Shadow and Maria looked at each other worriedly, but neither could think up a retort. There was a long pause.

"If you say so." The Ultimate Life Form marched up the stairs following Maria and the bat. "I hope you don't get too lonely."


End file.
